/* Function: free_GenomicDB(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [GenomicDB *]
*
* Return [UNKN ] Undocumented return value [GenomicDB *]
*
*/
GenomicDB * free_GenomicDB(GenomicDB * obj)
{
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a GenomicDB obj. Should be trappable");
return NULL;
}
if( obj->dynamite_hard_link > 1) {
obj->dynamite_hard_link--;
return NULL;
}
if( obj->forw != NULL)
free_ComplexSequence(obj->forw);
if( obj->rev != NULL)
free_ComplexSequence(obj->rev);
if( obj->sdb != NULL)
free_SequenceDB(obj->sdb);
if( obj->current != NULL)
free_Genomic(obj->current);
if( obj->cses != NULL)
free_ComplexSequenceEvalSet(obj->cses);
if( obj->single != NULL)
free_Genomic(obj->single);
if( obj->revsingle != NULL)
free_Genomic(obj->revsingle);
ckfree(obj);
return NULL;
}
/* Function: free_Gene(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [Gene *]
*
* Return [UNKN ] Undocumented return value [Gene *]
*
*/
Gene * free_Gene(Gene * obj)
{
int i;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a Gene obj. Should be trappable");
return NULL;
}
if( obj->dynamite_hard_link > 1) {
obj->dynamite_hard_link--;
return NULL;
}
/* obj->parent is linked in */
if( obj->genomic != NULL)
free_Genomic(obj->genomic);
if( obj->transcript != NULL) {
for(i=0;i<obj->len;i++) {
if( obj->transcript[i] != NULL)
free_Transcript(obj->transcript[i]);
}
ckfree(obj->transcript);
}
if( obj->name != NULL)
ckfree(obj->name);
if( obj->seqname != NULL)
ckfree(obj->seqname);
ckfree(obj);
return NULL;
}
void reverse_target(void)
{
Genomic * gen_temp;
gen_temp = reverse_complement_Genomic(gen);
free_temporary_objects();
free_Genomic(gen);
gen = gen_temp;
}
boolean close_GenomicDB(ComplexSequence * cs,GenomicDB * gendb)
{
if( gendb->is_single_seq == TRUE ) {
return TRUE;
}
if( cs != NULL)
free_ComplexSequence(cs);
if( gendb->current != NULL)
gendb->current = free_Genomic(gendb->current);
return close_SequenceDB(NULL,gendb->sdb);
}
/* Function: free_Gene(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [Gene *]
*
* Return [UNKN ] Undocumented return value [Gene *]
*
*/
Gene * free_Gene(Gene * obj)
{
int return_early = 0;
int i;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a Gene obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
/* obj->parent is linked in */
if( obj->genomic != NULL)
free_Genomic(obj->genomic);
if( obj->transcript != NULL) {
for(i=0;i<obj->len;i++) {
if( obj->transcript[i] != NULL)
free_Transcript(obj->transcript[i]);
}
ckfree(obj->transcript);
}
if( obj->name != NULL)
ckfree(obj->name);
if( obj->seqname != NULL)
ckfree(obj->seqname);
ckfree(obj);
return NULL;
}
boolean free_io_objects(void)
{
if( use_tsm == TRUE) {
free_ThreeStateModel(tsm);
} else {
free_Protein(pro);
}
free_CodonTable(ct);
if( gf != NULL ) {
free_GeneFrequency21(gf);
}
free_RandomModelDNA(rmd);
if( is_embl ) {
free_GenomicRegion(embl);
}
free_Genomic(gen);
return TRUE;
}
boolean build_objects(void)
{
boolean ret = TRUE;
Protein * pro_temp;
Genomic * gen_temp;
FILE * ifp;
startend = threestatemodel_mode_from_string(startend_string);
if( startend == TSM_unknown ) {
warn("String %s was unable to converted into a start/end policy\n",startend_string);
ret = FALSE;
}
if( tstart_str != NULL ) {
if( is_integer_string(tstart_str,&tstart) == FALSE || tstart < 0) {
warn("Could not make %s out as target start",tstart);
ret = FALSE;
}
}
if( tend_str != NULL ) {
if( is_integer_string(tend_str,&tend) == FALSE || tend < 0) {
warn("Could not make %s out as target end",tend);
ret = FALSE;
}
}
if( is_integer_string(gap_str,&gap) == FALSE ) {
warn("Could not make %s out as gap penalty (must be integer at the moment)",gap_str);
ret = FALSE;
}
if( is_integer_string(ext_str,&ext) == FALSE ) {
warn("Could not make %s out as gap penalty (must be integer at the moment)",ext_str);
ret = FALSE;
}
if( is_embl == FALSE ) {
if( (gen = read_fasta_file_Genomic(dna_seq_file,length_of_N)) == NULL ) {
ret = FALSE;
warn("Could not read genomic sequence in %s",dna_seq_file);
gen = NULL;
}
} else {
embl = read_EMBL_GenomicRegion_file(dna_seq_file);
if( embl == NULL ) {
warn("Could not read genomic EMBL file in %s",dna_seq_file);
gen = NULL;
ret = FALSE;
} else {
gen = hard_link_Genomic(embl->genomic);
}
}
if( gen != NULL ) {
if( tstart != -1 || tend != -1 ) {
if( tstart == -1 )
tstart = 0;
if( tend == -1 )
tend = gen->baseseq->len;
gen_temp = truncate_Genomic(gen,tstart-1,tend);
if( gen_temp == NULL ){
ret = FALSE;
} else {
free_Genomic(gen);
gen = gen_temp;
}
} else {
/* no truncation required */
}
if( reverse == TRUE ) {
if( tstart > tend ) {
warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
}
gen_temp = reverse_complement_Genomic(gen);
free_Genomic(gen);
gen = gen_temp;
}
}
/*
* Can't truncate on GenomicRegion (for good reasons!).
* but we want only a section of the EMBL file to be used
*
* So... swap genomic now. Positions in EMBL are still valid,
* however - some genes will loose their sequence, which will be damaging. ;)
*/
if( is_embl ) {
free_Genomic(embl->genomic);
embl->genomic = hard_link_Genomic(gen); /* pointer could be dead anyway ;) */
}
if( target_abs == TRUE ) {
if( is_embl == TRUE ) {
warn("Sorry you can't both use absolute positioning and EMBL files as I can't cope with all the coordinate remapping. You'll have to convert to fasta.");
ret = FALSE;
}
gen->baseseq->offset = 1;
gen->baseseq->end = strlen(gen->baseseq->seq);
}
if( alg_str != NULL ) {
alg = gwrap_alg_type_from_string(alg_str);
} else {
if( use_tsm == TRUE ) {
alg_str = "623L";
} else {
alg_str = "623";
}
alg = gwrap_alg_type_from_string(alg_str);
}
if( qstart_str != NULL ) {
if( is_integer_string(qstart_str,&qstart) == FALSE || qstart < 0) {
warn("Could not make %s out as query start",qstart);
ret = FALSE;
}
}
if( qend_str != NULL ) {
if( is_integer_string(qend_str,&qend) == FALSE || qend < 0) {
warn("Could not make %s out as query end",qend);
ret = FALSE;
}
}
if( use_tsm == FALSE ) {
if( startend != TSM_default && startend != TSM_global && startend != TSM_local && startend != TSM_endbiased) {
warn("Proteins can only have local/global/endbias startend policies set, not %s",startend_string);
ret = FALSE;
}
if( (pro = read_fasta_file_Protein(protein_file)) == NULL ) {
ret = FALSE;
warn("Could not read Protein sequence in %s",protein_file);
} else {
if( qstart != -1 || qend != -1 ) {
if( qstart == -1 )
qstart = 0;
if( qend == -1 )
qend = pro->baseseq->len;
pro_temp = truncate_Protein(pro,qstart-1,qend);
if( pro_temp == NULL ){
ret = FALSE;
} else {
free_Protein(pro);
pro = pro_temp;
}
}
}
} else {
/** using a HMM **/
/*tsm = read_HMMer_1_7_ascii_file(hmm_file);*/
/*tsm = Wise2_read_ThreeStateModel_from_hmmer1_file(hmm_file);*/
tsm = HMMer2_read_ThreeStateModel(hmm_file);
if( tsm == NULL ) {
warn("Could not read hmm from %s\n",hmm_file);
ret = FALSE;
} else {
display_char_in_ThreeStateModel(tsm);
if( hmm_name != NULL ) {
if( tsm->name != NULL )
ckfree(tsm->name);
tsm->name = stringalloc(hmm_name);
}
if( tsm == NULL ) {
warn("Could not read %s as a hmm",hmm_file);
}
/** have to set start/end **/
set_startend_policy_ThreeStateModel(tsm,startend,30,0.1);
}
} /* end of else tsm != NULL */
if( main_block_str != NULL ) {
if( is_integer_string(main_block_str,&main_block) == FALSE ) {
warn("Could not get maximum main_block number %s",main_block_str);
ret = FALSE;
}
}
if( is_double_string(subs_string,&subs_error) == FALSE ) {
warn("Could not convert %s to a double",subs_error);
ret = FALSE;
}
if( is_double_string(indel_string,&indel_error) == FALSE ) {
warn("Could not convert %s to a double",indel_error);
ret = FALSE;
}
if( is_double_string(allN_string,&allN) == FALSE ) {
warn("Could not convert %s to a double",allN_string);
ret = FALSE;
}
if( strcmp(cfreq_string,"model") == 0 ) {
model_codon = TRUE;
} else if ( strcmp(cfreq_string,"flat") == 0 ) {
model_codon = FALSE;
} else {
warn("Cannot interpret [%s] as a codon modelling parameter\n",cfreq_string);
ret = FALSE;
}
if( strcmp(splice_string,"model") == 0 ) {
model_splice = TRUE;
} else if ( strcmp(splice_string,"flat") == 0 ) {
model_splice = FALSE;
gmp->use_gtag_splice = TRUE;
} else {
warn("Cannot interpret [%s] as a splice modelling parameter\n",splice_string);
ret = FALSE;
}
if( strcmp(null_string,"syn") == 0 ) {
use_syn = TRUE;
} else if ( strcmp(null_string,"flat") == 0 ) {
use_syn = FALSE;
} else {
warn("Cannot interpret [%s] as a null model string\n",null_string);
ret = FALSE;
}
if( strcmp(intron_string,"model") == 0 ) {
use_tied_model = FALSE;
} else if ( strcmp(intron_string,"tied") == 0 ) {
use_tied_model = TRUE;
} else {
warn("Cannot interpret [%s] as a intron tieing switch\n",intron_string);
ret = FALSE;
}
if( (rm = default_RandomModel()) == NULL) {
warn("Could not make default random model\n");
ret = FALSE;
}
if( use_new_stats == 0 ) {
if( (gf = read_GeneFrequency21_file(gene_file)) == NULL) {
ret = FALSE;
warn("Could not read a GeneFrequency file in %s",gene_file);
}
} else {
if( (gs = GeneStats_from_GeneModelParam(gmp)) == NULL ){
ret=FALSE;
warn("Could not read gene statistics in %s",new_gene_file);
}
} /* end of else using new gene stats */
if( (mat = read_Blast_file_CompMat(matrix_file)) == NULL) {
if( use_tsm == TRUE ) {
info("I could not read the Comparison matrix file in %s; however, you are using a HMM so it is not needed. Please set the WISECONFIGDIR or WISEPERSONALDIR variable correctly to prevent this message.",matrix_file);
} else {
warn("Could not read Comparison matrix file in %s",matrix_file);
ret = FALSE;
}
}
if( (ct = read_CodonTable_file(codon_file)) == NULL) {
ret = FALSE;
warn("Could not read codon table file in %s",codon_file);
}
if( (ofp = openfile(output_file,"W")) == NULL) {
warn("Could not open %s as an output file",output_file);
ret = FALSE;
}
rmd = RandomModelDNA_std();
return ret;
}
ComplexSequence * reload_GenomicDB(ComplexSequence * last,GenomicDB * gendb,int * return_status)
{
ComplexSequence * cs;
Sequence * seq;
Genomic *temp;
Genomic * gen;
/** NB - notice that we don't do silly things with free's. Maybe we should **/
if( gendb->is_single_seq == TRUE ) {
if( gendb->done_forward == TRUE ) {
*return_status = DB_RETURN_OK;
gendb->done_forward = FALSE;
return hard_link_ComplexSequence(gendb->rev);
} else {
*return_status = DB_RETURN_END;
return NULL;
}
}
/** standard database **/
/** free Complex Sequence **/
if ( last != NULL ) {
free_ComplexSequence(last);
}
if( gendb->done_forward == TRUE ) {
if( gendb->current == NULL ) {
warn("A bad internal genomic db error - unable to find current sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
temp = reverse_complement_Genomic(gendb->current);
if( temp == NULL ) {
warn("A bad internal genomic db error - unable to reverse complements current");
*return_status = DB_RETURN_ERROR;
return NULL;
}
cs = evaluate_ComplexSequence_Genomic(temp,gendb->cses,0,gendb->repeat_in_cds_score);
if( cs == NULL ) {
warn("A bad internal genomic db error - unable to make complex sequence in db reload");
*return_status = DB_RETURN_ERROR;
return NULL;
}
free_Genomic(temp);
gendb->done_forward = FALSE;
return cs;
}
/* otherwise we have to get a new sequence */
seq = reload_SequenceDB(NULL,gendb->sdb,return_status);
if( seq == NULL || *return_status == DB_RETURN_ERROR || *return_status == DB_RETURN_END ) {
return NULL; /** error already reported **/
}
uppercase_Sequence(seq);
/* check dna status. We assumme someone knows what he is doing when he makes a genomic db!*/
if( seq->type != SEQUENCE_DNA) {
warn("Sequence from %s data entry doesn't look like DNA. Forcing it to",seq->name);
}
force_to_dna_Sequence(seq,1.0,NULL);
if( force_to_dna_Sequence(seq,0.1,NULL) == FALSE ) {
if( gendb->error_handling == GENDB_READ_THROUGH ) {
warn("Unable to map %s sequence to a genomic sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_GenomicDB(NULL,gendb,return_status);
} else {
warn("Unable to map %s sequence to a genomic sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
gen = Genomic_from_Sequence_Nheuristic(seq,gendb->length_of_N);
cs = evaluate_ComplexSequence_Genomic(gen,gendb->cses,0,gendb->repeat_in_cds_score);
if( cs == NULL ) {
if( gendb->error_handling == GENDB_READ_THROUGH ) {
warn("Unable to map %s sequence to a genomic sequence, but ignoring that for the moment...",seq->name);
free_Sequence(seq);
return reload_GenomicDB(NULL,gendb,return_status);
} else {
warn("Unable to map %s sequence to a genomic sequence. Failing",seq->name);
*return_status = DB_RETURN_ERROR;
return NULL;
}
}
gendb->current = free_Genomic(gendb->current);
gendb->current = gen;
gendb->done_forward= TRUE;
return cs;
}